org.biojava.bio.structure
Interface Atom

All Known Implementing Classes:

AtomImpl

public interface Atom

simple interface of an Atom.

Since:

1.4

Version:

%I% %G%

Author:

Andreas Prlic, Horvath Tamas

Method Summary

Object	clone() returns and identical copy of this object .
Character	getAltLoc() get set alternate Location.
double[]	getCoords() get the coordinates.
String	getFullName() get full name of atom e.g.
String	getName() get trimmed version of atom name, e.g.
double	getOccupancy() get occupancy.
Group	getParent() Returns the parent Group of the Atom returns null if the referenced object is not Group
String	getPDBline() store the whole line.
int	getPDBserial() get PDB atom number.
double	getTempFactor() get set temp factor.
double	getX() get cordinate X.
double	getY() get cordinate Y.
double	getZ() get cordinate Z.
void	setAltLoc(Character c) get set alternate Location.
void	setCoords(double[] c) set the coordinates.
void	setFullName(String s) set full name of atom e.g.
void	setName(String s) set trimmed version of atom name, e.g.
void	setOccupancy(double occupancy) set occupancy.
void	setParent(Group parent) Sets the back-reference to its parent Group
void	setPDBline(String s) store the whole line.
void	setPDBserial(int i) set PDB atom number.
void	setTempFactor(double temp) get set temp factor .
void	setX(double x) set the X coordinate
void	setY(double y) set the Y coordinate
void	setZ(double z) set the Z coordinate

Method Detail

setName

void setName(String s)

set trimmed version of atom name, e.g. "CA".

Parameters:

s - a String specifying the name value

See Also:

getName()

getName

String getName()

get trimmed version of atom name, e.g. "CA".

Returns:

a String representing the name value

See Also:

setName(java.lang.String)

setFullName

void setFullName(String s)

set full name of atom e.g. " CA ".

Parameters:

s - a String specifying the full name value

See Also:

getFullName()

getFullName

String getFullName()

get full name of atom e.g. " CA ".

Returns:

a String representing the full name value

See Also:

setFullName(java.lang.String)

setPDBserial

void setPDBserial(int i)

set PDB atom number.

Parameters:

i - an int specifying the PDBserial value

See Also:

getPDBserial()

getPDBserial

int getPDBserial()

get PDB atom number.

Returns:

an int representing the PDBserial value

See Also:

setPDBserial(int)

setCoords

void setCoords(double[] c)

set the coordinates.

Parameters:

c - an array of doubles specifying the coords value

See Also:

getCoords()

getCoords

double[] getCoords()

get the coordinates.

Returns:

an array of doubles representing the coords value

See Also:

setCoords(double[])

setX

void setX(double x)

set the X coordinate

Parameters:

x - a double

setY

void setY(double y)

set the Y coordinate

Parameters:

y - a double

setZ

void setZ(double z)

set the Z coordinate

Parameters:

z - a double

getX

double getX()

get cordinate X.

Returns:

a double

getY

double getY()

get cordinate Y.

Returns:

a double

getZ

double getZ()

get cordinate Z.

Returns:

a double

setAltLoc

void setAltLoc(Character c)

get set alternate Location.

Parameters:

c - a Character object specifying the alt loc value

See Also:

getAltLoc()

getAltLoc

Character getAltLoc()

get set alternate Location.

Returns:

a Character object representing the alt loc value

See Also:

setAltLoc(java.lang.Character)

setPDBline

void setPDBline(String s)

store the whole line.

Parameters:

s - a String specifying the PDBline value

See Also:

getPDBline()

getPDBline

String getPDBline()

store the whole line.

Returns:

a String representing the PDBline value

See Also:

setPDBline(java.lang.String)

setOccupancy

void setOccupancy(double occupancy)

set occupancy.

Parameters:

occupancy - a double specifying the occupancy value

See Also:

getOccupancy()

getOccupancy

double getOccupancy()

get occupancy.

Returns:

a double representing the occupancy value

See Also:

setOccupancy(double)

setTempFactor

void setTempFactor(double temp)

get set temp factor .

Parameters:

temp - a double specifying the temp factor value

See Also:

getTempFactor()

getTempFactor

double getTempFactor()

get set temp factor.

Returns:

a double representing the temp factor value

See Also:

setTempFactor(double)

clone

Object clone()

returns and identical copy of this object .

Returns:

and identical copy of this object

setParent

void setParent(Group parent)

Sets the back-reference to its parent Group

Parameters:

parent - the parent Group

getParent

Group getParent()

Returns the parent Group of the Atom returns null if the referenced object is not Group

Returns:

Group the parent Group of the Atom, or null